PDB -> SwissPROT conversion?

Paul Davis Paul at pdchem.demon.co.uk
Fri Jun 5 10:58:16 EST 1998


In article <6l7588$j4n$1 at netnews.upenn.edu>
           alwang at blue.seas.upenn.edu "Al Wang" writes:

> Does anyone know what's a good way to take a Brookhaven PDB file, extract 
> the sequence information, and save it in SwissPROT format?  If it can 
> also extract the secondary structure features, even better.  
> 

The program STRIDE by Frishman and Argos, which I obtained
from

http://www.embl-heidelberg.de/argos/stride/stride_info.html

will generate secondary structure assignments from the
atomic coordinates in a PDB file.  While the assignments
will not always correspond exactly to the HELIX, SHEET and
TURN records of a PDB file (where these are present), they
are made in a consistent manner and are possibly more useful
in comparative studies.

STRIDE can also output the sequence in fasta format.

See Proteins 23: 566-579 (1995)

-Paul
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Paul Davis                                   paul at pdchem.demon.co.uk





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